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CylinderPhantom.py
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CylinderPhantom.py
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# encoding: utf-8
import egsnrc.EGSPhant as EGSPhant
from numarray import *
# want to make a phantom used in skindose
# the lower section is oblongoid:
# height 5cm
# width 20cm
# depth 30cm
# the upper section is a half-cylinder (semicircular prism)
# radius 10cm
# depth 30cm
#
# so, 3 parameters define its size: height, radius, depth
# (width = 2 x radius)
# also need to define voxel size dx, dy, dz
# NB x-coord is read from left to right,
# y-coord from top to bottom
# z-coord from top to bottom
class CylinderPhantom:
def __init__(self, filename=None):
self.debug_p = False
self.phantfilename = filename
# all measurements are in cm
self.height = 5.
self.radius = 10.
self.width = 2. * self.radius
self.depth = 30.
# voxel size
self.dx = 0.05
self.dy = 0.05
self.dz = 0.25
# compute dimensions of phantom, i.e. number of
# voxels in each direction
self.dimensions = (int(self.width / self.dx), \
int((self.height + self.radius) / self.dy), \
int(self.depth / self.dz))
# print self.dimensions
# make a blank phantom
self.phantom = EGSPhant.EGSPhant(None, self.dimensions[0], self.dimensions[1], self.dimensions[2])
self.phantom.phantfilename = self.phantfilename
# phantom is just air and water
self.phantom.nmaterials = 2
self.phantom.materials = ('AIR700ICRU', 'H2O700ICRU')
self.phantom.estepe = ones(self.phantom.nmaterials, type=Float32)
# set the voxel edges
self.phantom.xedges = zeros(self.phantom.dimensions[0]+1, type=Float32)
self.phantom.yedges = zeros(self.phantom.dimensions[1]+1, type=Float32)
self.phantom.zedges = zeros(self.phantom.dimensions[2]+1, type=Float32)
for i in range(self.phantom.dimensions[0]+1):
self.phantom.xedges[i] = -10. + i * self.dx
for i in range(self.phantom.dimensions[1]+1):
self.phantom.yedges[i] = -10. + i * self.dy
for i in range(self.phantom.dimensions[2]+1):
self.phantom.zedges[i] = -15. + i * self.dz
self.phantom.edges_to_centers()
def build(self):
# all slices are air
self.phantom.materialscan = ones([self.phantom.dimensions[2],
self.phantom.dimensions[1], self.phantom.dimensions[0]],
type=Int32)
# we'll fix the density scan after the phantom is built up
self.phantom.densityscan = zeros([self.phantom.dimensions[2],
self.phantom.dimensions[1], self.phantom.dimensions[0]],
type=Float32)
#
# now, make the cylinder shape
#
# first, the easy bit: the oblong part at the bottom
# it covers all x, all z, and part of y
j_start = int(self.radius / self.dy)
self.phantom.materialscan[:,j_start:,:] = 2 * ones([self.phantom.dimensions[2],
int(self.height / self.dy), self.phantom.dimensions[0]], type=Int32)
# take the constant-z slices
# in the first slice,
# if the distance from the voxel to (0,0,z) is less than self.radius,
# set that voxel to have material 2 (water)
# copy that first slice to all other slices
j_max = int(self.radius / self.dy)
for j in range(j_max):
for i in range(self.phantom.dimensions[0]):
if self.distance(self.phantom.x[i], self.phantom.y[j], 0., 0.) < self.radius:
self.phantom.materialscan[0,j,i] = 2
# all the slices are the same
for k in range(1, self.phantom.dimensions[2]):
self.phantom.materialscan[k,:,:] = self.phantom.materialscan[0,:,:]
# fix up the density scan
self.phantom.fix_all_density()
self.phantom.save()
def read(self, filename=None):
self.debug_print("HERE WE ARE")
if (filename):
self.phantfilename = filename
self.phantom.read(self.phantfilename)
self.debug_print("CYL.PHANTOM: Done reading")
def distance(self, x1, y1, x2, y2):
dx = x1 - x2
dy = y1 - y2
return math.sqrt(dx*dx + dy*dy)
def debug_print(self, arg):
if self.debug_p:
print arg